In the talks, Obama is expected to try to sell his new strategy for Afghanistan and Pakistan, which includes proposals to counter a persistent Taliban and al-Qaeda campaign.
Obama will also "reaffirm US support of Turkey's bid to become a member of the EU", a US official said.
France, Austria and other nations oppose Turkey's long-running efforts to join the EU. Others in the organisation have urged Turkey to do more to guarantee minority rights, curb the powers of its military and pass new rights for trade unions.
While Turkey has been long regarded as a close US ally in the Muslim world, some analysts believe there has been a cooling of ties during the administration of George Bush, the former US president.
However, Obama hopes his visit will strengthen US-Turkish relations strained by the Iraq war.
Washington and Ankara had been sharply at odds in recent years over such issues as how to deal with Iran's nuclear programme, the rise to power of Hamas in the Palestinian territory of Gaza, and political developments in Sudan.
Al Jazeera's Anita McNaught, reporting from Istanbul, said: "What everyone wants to hear is how Obama will define new US ties with Turkey, because they are concerned that instability in Iraq may increase as the US pulls back, which could make Iraq their problem.
"At the same time, Turkey has enormous benefit in a peaceful and stable future for Iraq because while exports are down globally, Turkish exports to the re-nascent nation of Iraq are up 75 per cent," she said.
"That's not to mention the ongoing security agreement and a very critical emergent relationship between Turkey and the Kurdish autonomous region in northern Iraq," McNaught said.
While in Turkey, Obama will visit Istanbul to meet religious leaders, tour historical sites and hold a round-table meeting with university students.
He is also scheduled to attend a reception of the Alliance of Civilisations, a forum which aims to foster dialogue between the West and the Muslim world.
The Turkish authorities have taken unprecedented security measures in view of Obama's visit.
A street leading to the hotel where the US president is staying in Ankara has been blocked off. Military jets and police helicopters have been instructed to patrol the capital's skies.
There have been huge protests preceding Obama's visit across many Turkish cities.
Protestors said the US president was seeking to pressure Turkey to deploy troops in Afghanistan in an effort to control the situation there.